Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 6368-YMR297W | YMR297W | PRC1 | CPY1|carboxypeptidase C PRC1|CPY|LBC1 | Vacuolar carboxypeptidase Y (proteinase C, CPY); broad-specificity C-terminal exopeptidase involved in non-specific protein degradation in the vacuole; member of the serine carboxypeptidase family | Core | NA | NA | NA |
| 6369-YMR298W | YMR298W | LIP1 | sphingosine N-acyltransferase subunit LIP1 | Ceramide synthase subunit; single-span ER membrane protein associated with Lag1p and Lac1p and required for ceramide synthase activity, null mutant grows extremely slowly and is defective in ceramide synthesis | Core | NA | NA | NA |
| 6370-YMR299C | YMR299C | DYN3 | dynein light intermediate chain | Dynein light intermediate chain (LIC); localizes with dynein, null mutant is defective in nuclear migration | Core | NA | NA | NA |
| 6371-YMR300C | YMR300C | ADE4 | amidophosphoribosyltransferase | Phosphoribosylpyrophosphate amidotransferase (PRPPAT); catalyzes first step of the 'de novo' purine nucleotide biosynthetic pathway; also known as amidophosphoribosyltransferase | Core | NA | NA | NA |
| 6372-YMR301C | YMR301C | ATM1 | ATP-binding cassette Fe/S cluster precursor transporter ATM1 | Mitochondrial inner membrane ATP-binding cassette (ABC) transporter; exports mitochondrially synthesized precursors of iron-sulfur (Fe/S) clusters to the cytosol; human homolog ABCB7 can complement yeast null mutant | Core | NA | NA | NA |
| 6373-YMR302C | YMR302C | YME2 | PRP12|RNA12 | Integral inner mitochondrial membrane protein; role in maintaining mitochondrial nucleoid structure and number; mutants exhibit an increased rate of mitochondrial DNA escape; shows some sequence similarity to exonucleases | Core | NA | NA | NA |
| 6374-YMR303C | YMR303C | ADH2 | alcohol dehydrogenase ADH2|ADR2 | Glucose-repressible alcohol dehydrogenase II; catalyzes the conversion of ethanol to acetaldehyde; involved in the production of certain carboxylate esters; regulated by ADR1 | Accessory | Ancestral | NA | NA |
| 6375-YMR304C-A | YMR304C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps 3' end of verified ORF SCW10/YMR305C | Accessory | Ancestral | NA | NA |
| 6376-YMR304W | YMR304W | UBP15 | ubiquitin-specific protease UBP15 | Ubiquitin-specific protease involved in protein deubiquitination; forms a complex with AAA peroxins Pex1p and Pex6p; deubiquitinates mono- and polyubiquitinated forms of Pex5p; deubiquitinates Clb5p, counteracting APC activity, and facilitating both Clb5p accumulation and S phase entry; physically interacts with anaphase-promoting complex/cyclosome (APC/C) activator, Cdh1p; catalytic activity regulated by an N-terminal TRAF-like domain and and C-terminal sequences | Core | NA | NA | NA |
| 6377-YMR305C | YMR305C | SCW10 | putative family 17 glucosidase | Cell wall protein with similarity to glucanases; may play a role in conjugation during mating based on mutant phenotype and its regulation by Ste12p; SWC10 has a paralog, SCW4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6378-YMR306W_NumOfGenes_2 | YMR306W | FKS3 | putative 1,3-beta-D-glucan synthase | Protein involved in spore wall assembly; has similarity to 1,3-beta-D-glucan synthase catalytic subunits Fks1p and Gsc2p; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6379-YMR307W_NumOfGenes_2 | YMR307W | GAS1 | 1,3-beta-glucanosyltransferase GAS1|GGP1|CWH52 | Beta-1,3-glucanosyltransferase; required for cell wall assembly and also has a role in transcriptional silencing; localizes to cell surface via a glycosylphosphatidylinositol (GPI) anchor; also found at nuclear periphery; genetic interactions with histone H3 lysine acetyltransferases GCN5 and SAS3 indicate previously unsuspected functions for Gas1 in DNA damage response and cell cycle regulation | Accessory | Ancestral | NA | NA |
| 6380-YMR308C | YMR308C | PSE1 | KAP121 | Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p | Core | NA | NA | NA |
| 6381-YMR309C | YMR309C | NIP1 | translation initiation factor eIF3 core subunit c | eIF3c subunit of the eukaryotic translation initiation factor 3 (eIF3); involved in the assembly of preinitiation complex and start codon selection; eIF3 is also involved in programmed stop codon readthrough | Core | NA | NA | NA |
| 6382-YMR310C | YMR310C | NA | putative methyltransferase | Putative methyltransferase; predicted to be involved in ribosome biogenesis; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; not an essential gene; YMR310C has a paralog, YGR283C, that arose from the whole genome duplication | Core | NA | NA | NA |